I'm have the same situation with large tables. Take a look at using a
cursor to fetch several thousand rows at a time. I presume what's
happening is that perl is attempting to create a massive list/array in
memory. If you use a cursor the list should only contain X number of
rows where X in the number specified at each fetch execution. You'll
need to define the cursor inside a transaction block.
- begin transaction
- define the cursor
- fetch rows from cursor
- while row count from previous step > 0, execute previous step
- terminate transaction
Or you could use plpgsql instead of plperl, FOR loops over result sets in
plpgsql implicitly use cursors... it's just a little less code.
Hope that helps,
Wayne
On Tue, Jul 05, 2011 at 10:29:03PM +0200, Viktor Bojovi?? wrote:
> Hi,
> while reading 20GB table through PL/PERL function , it constantly grows in
> RAM.
> I wanted to ask you which is the best way to read table inside that
> function without such memory consumption.
> Thanks in advance
>
> Code is here:
>
> CREATE FUNCTION pattern_counter("patLength" integer)
> RETURNS varchar AS
> $BODY$
> my $rv = spi_exec_query("select sequence from entry");
> my $rowCount = $rv->{processed};
> my $patLen = $_[0];
> my $patt = '';
> my %patterns=();
> foreach my $rn (0 .. $rowCount -1){
> my $row = $rv->{rows}[$rn];
> my $seq = $row->{sequence};
> for (my $x = 1;$x<=length($seq) - $patLen;$x++){
> $patt=substr($seq,$x,$patLen);
> if (! defined $patterns{$patt}) {
> $patterns{$patt}=1;
> }else{
> $patterns{$patt}++;
> }
> }
> }
> foreach $patt (keys %patterns){
> my $sql="insert into patterns values('".$patt."',".$patterns{$patt}.")";
> spi_exec_query($sql);
> }
> return '';
> $BODY$
> LANGUAGE plperl VOLATILE
> COST 100;
>
>
>
> --
> ---------------------------------------
> Viktor Bojovi??
> ---------------------------------------
> Wherever I go, Murphy goes with me
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